Evolution of protein families: is it possible to distinguish between domains of life?
Evolution of protein families: is it possible to distinguish between domains of life?
复制标题
蛋白质家族的进化：是否有可能区分生命领域？
DOI：
10.1016/j.gene.2007.07.029
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发表时间：
2007
期刊：
影响因子：
3.5
通讯作者：
Guimerà,Roger
中科院分区：
文献类型：
--
作者：
Sales-Pardo,Marta;Chan,AlbertOB;Amaral,LuísAN;Guimerà,Roger
了解物种之间的进化关系可以为生命之树的根源和真核生物的起源提供新的线索，从而引起人们对在十亿年左右的时间尺度上准确评估进化参数的长期兴趣。先前的工作表明分子替代率存在很大的变异性，然而，我们仍然不知道这种变异性是否是由于基因组规模上的物种特异性趋势造成的，或者是否可以归因于任何随机过程中固有的波动。在这里，我们研究基因和蛋白质家族大小的统计特性，以量化跨物种的长期进化差异和相似性。我们首先确定了 209 种细菌和 20 种古细菌的蛋白质家族。我们发现我们无法拒绝这些物种的蛋白质家族大小来自相同分布的零假设。此外，我们发现，对于属于同一系统发育分支或同一生活方式组的物种，科规模分布并不比不同分支的物种更相似。这两项发现可以用动态出生、死亡和创新模型来解释，该模型假设所有物种的蛋白质家族进化率相同。因此，我们的理论和经验结果强烈表明，在蛋白质家族大小分布中经验观察到的变异性与具有相同基因组进化速率的进化过程的预期随机波动相一致。我们的研究结果对于某些真核生物起源理论的合理性具有特别重要的意义，这些理论需要在过去 20 亿年的某个时期内进化速率发生巨大变化。
Understanding evolutionary relationships between species can shed new light into the rooting of the tree of life and the origin of eukaryotes, thus, resulting in a long standing interest in accurately assessing evolutionary parameters at time scales on the order of a billion of years. Prior work suggests large variability in molecular substitution rates, however, we still do not know whether such variability is due to species-specific trends at a genomic scale, or whether it can be attributed to the fluctuations inherent in any stochastic process. Here, we study the statistical properties of gene and protein-family sizes in order to quantify the long time scale evolutionary differences and similarities across species. We first determine the protein families of 209 species of bacteria and 20 species of archaea. We find that we are unable to reject the null hypothesis that the protein-family sizes of these species are drawn from the same distribution. In addition, we find that for species classified in the same phylogenetic branch or in the same lifestyle group, family size distributions are not significantly more similar than for species in different branches. These two findings can be accounted for in terms of a dynamical birth, death, and innovation model that assumes identical protein-family evolutionary rates for all species. Our theoretical and empirical results thus strongly suggest that the variability empirically observed in protein-family size distributions is compatible with the expected stochastic fluctuations for an evolutionary process with identical genomic evolutionary rates. Our findings hold special importance for the plausibility of some theories of the origin of eukaryotes which require drastic changes in evolutionary rates for some period during the last 2 billion years.